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gxiaolab / isoLASER

MIT License
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Read-level phasing results in output? #2

Open camelest opened 1 month ago

camelest commented 1 month ago

Hi, thank you so much for the great tool!

I was wondering whether we could obtain read-level phasing result for the input bam. I checked the test_pipeline output but I think we only have isoform-level information as shown below.

$ head isolaser.dlpfc_1.mi_summary.tab -n 5
#chrom  start   end     strand  Gene_name       Linkage_Type    PG      AMI     chi_p   Cov     PSI     AR      allelic_counts  label   Delta_PSI
chr21   25639257        25715896        +       ENSG00000154721.15_JAM2 ASTS    HAP-0   nan     nan     25      nan     1.000   nan     nan     nan
chr21   25706086        25706100        +       ENSG00000154721.15_JAM2 HAP-ExonicPart  HAP-0   nan     nan     25      0.000   1.000   25;0;0;0        nan     nan
chr21   25709433        25709449        +       ENSG00000154721.15_JAM2 HAP-ExonicPart  HAP-0   nan     nan     25      1.000   1.000   0;25;0;0        nan     nan
chr21   25706086        25706100        +       ENSG00000154721.15_JAM2 VAR     chr21:[25639639,25639643)/.     nan     nan     10      0.000   0.000   10;0;0;0        nan     nan

Thank you so much for your help!

giovanniquinones commented 1 month ago

Hi, Thank you for your interest in our tool. Please be advised that the corresponding manuscript is under review, and we will be changing and updating the source code. We will take this issue into account for the next release.

camelest commented 1 month ago

Thank you so much for the consideration!